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Dhakephalkar T, Stukey G, Guan Z, Carman GM, Klein EA. Characterization of an evolutionarily distinct bacterial ceramide kinase from Caulobacter crescentus. J Biol Chem 2023:104894. [PMID: 37286040 PMCID: PMC10331486 DOI: 10.1016/j.jbc.2023.104894] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/27/2023] [Accepted: 06/01/2023] [Indexed: 06/09/2023] Open
Abstract
A common feature among nearly all Gram-negative bacteria is the requirement for lipopolysaccharide (LPS) in the outer leaflet of the outer membrane. LPS provides structural integrity to the bacterial membrane which aids bacteria in maintaining their shape and acts as a barrier from environmental stress and harmful substances such as detergents and antibiotics. Recent work has demonstrated that Caulobacter crescentus can survive without LPS due to the presence of the anionic sphingolipid ceramide-phosphoglycerate. Based on genetic evidence, we predicted that protein CpgB functions as a ceramide kinase and performs the first step in generating the phosphoglycerate head group. Here, we characterized the kinase activity of recombinantly expressed CpgB and demonstrated that it can phosphorylate ceramide to form ceramide 1-phosphate. The pH optimum for CpgB was 7.5, and the enzyme required Mg2+ as a cofactor. Mn2+, but not other divalent cations, could substitute for Mg2+. Under these conditions, the enzyme exhibited typical Michaelis-Menten kinetics with respect to NBD-C6-ceramide (Km,app=19.2 ± 5.5 μM; Vmax,app=2590 ± 230 pmol/min/mg enzyme) and ATP (Km,app=0.29 ± 0.07 mM; Vmax,app=10100 ± 996 pmol/min/mg enzyme). Phylogenetic analysis of CpgB revealed that CpgB belongs to a new class of ceramide kinases which is distinct from its eukaryotic counterpart; furthermore, the pharmacological inhibitor of human ceramide kinase (NVP-231) had no effect on CpgB. The characterization of a new bacterial ceramide kinase opens avenues for understanding the structure and function of the various microbial phosphorylated sphingolipids.
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Affiliation(s)
| | - Geordan Stukey
- Department of Food Science, Rutgers University, New Brunswick, NJ 08901, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food Nutrition and Health, Rutgers University, New Brunswick, NJ 08901, USA
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - George M Carman
- Department of Food Science, Rutgers University, New Brunswick, NJ 08901, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food Nutrition and Health, Rutgers University, New Brunswick, NJ 08901, USA
| | - Eric A Klein
- Biology Department, Rutgers University-Camden, Camden, NJ 08102, USA; Department of Food Science, Rutgers University, New Brunswick, NJ 08901, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food Nutrition and Health, Rutgers University, New Brunswick, NJ 08901, USA; Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ 08102, USA.
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Dhakephalkar T, Stukey G, Guan Z, Carman GM, Klein EA. Characterization of an evolutionarily distinct bacterial ceramide kinase from Caulobacter crescentus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.01.538943. [PMID: 37205603 PMCID: PMC10187206 DOI: 10.1101/2023.05.01.538943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A common feature among nearly all Gram-negative bacteria is the requirement for lipopolysaccharide (LPS) in the outer leaflet of the outer membrane. LPS provides structural integrity to the bacterial membrane which aids bacteria in maintaining their shape and acts as a barrier from environmental stress and harmful substances such as detergents and antibiotics. Recent work has demonstrated that Caulobacter crescentus can survive without LPS due to the presence of the anionic sphingolipid ceramide-phosphoglycerate. Based on genetic evidence, we predicted that protein CpgB functions as a ceramide kinase and performs the first step in generating the phosphoglycerate head group. Here, we characterized the kinase activity of recombinantly expressed CpgB and demonstrated that it can phosphorylate ceramide to form ceramide 1-phosphate. The pH optimum for CpgB was 7.5, and the enzyme required Mg 2+ as a cofactor. Mn 2+ , but not other divalent cations, could substitute for Mg 2+ . Under these conditions, the enzyme exhibited typical Michaelis-Menten kinetics with respect to NBD-C6-ceramide (K m,app =19.2 ± 5.5 μM; V max,app =2586.29 ± 231.99 pmol/min/mg enzyme) and ATP (K m,app =0.29 ± 0.07 mM; V max,app =10067.57 ± 996.85 pmol/min/mg enzyme). Phylogenetic analysis of CpgB revealed that CpgB belongs to a new class of ceramide kinases which is distinct from its eukaryotic counterpart; furthermore, the pharmacological inhibitor of human ceramide kinase (NVP-231) had no effect on CpgB. The characterization of a new bacterial ceramide kinase opens avenues for understanding the structure and function of the various microbial phosphorylated sphingolipids.
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3
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Ma Q, Srinivasan L, Gabelli SB, Raben DM. Elusive structure of mammalian DGKs. Adv Biol Regul 2022; 83:100847. [PMID: 34922895 PMCID: PMC8858910 DOI: 10.1016/j.jbior.2021.100847] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 01/03/2023]
Abstract
Mammalian diacylglycerol kinases (DGKs) are a group of enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol (DAG) to produce phosphatidic acid (PtdOH). In doing so, they modulate the levels of these two important signaling lipids. Currently, ten mammalian DGKs are organized into five classes that vary with respect to domain organization, regulation, and cellular/subcellular distribution. As lipids play critical roles in cells, it is not surprising that there is increasing interest in understanding the mechanism underlying the catalysis and regulation of lipid modulating enzymes such as DGKs. However, there are no solved 3D structures for any of the eukaryotic DGKs. In this review, we summarize what is known and the current challenges in determining the structures of these important enzymes. In addition to gain critical insights into their mechanisms of catalysis and regulation, DGK structures will provide a platform for the design of isoform specific inhibitors.
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Affiliation(s)
- Qianqian Ma
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore Maryland
| | - Lakshmi Srinivasan
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore Maryland
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore Maryland,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore Maryland,Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore Maryland,Corresponding author: Sandra B. Gabelli (), Daniel M. Raben ()
| | - Daniel M. Raben
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore Maryland,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore Maryland,Corresponding author: Sandra B. Gabelli (), Daniel M. Raben ()
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4
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Magli E, Corvino A, Fiorino F, Frecentese F, Perissutti E, Saccone I, Santagada V, Caliendo G, Severino B. Design of Sphingosine Kinases Inhibitors: Challenges and Recent Developments. Curr Pharm Des 2020; 25:956-968. [PMID: 30947653 DOI: 10.2174/1381612825666190404115424] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 03/27/2019] [Indexed: 12/28/2022]
Abstract
BACKGROUND Sphingosine kinases (SphKs) catalyze the phosphorylation of sphingosine to form the bioactive sphingolipid metabolite sphingosine-1-phosphate (S1P). S1P is an important lipid mediator with a wide range of biological functions; it is also involved in a variety of diseases such as inflammatory diseases, Alzheimer's disease and cancer. METHODS This review reports the recent advancement in the research of SphKs inhibitors. Our purpose is also to provide a complete overview useful for underlining the features needed to select a specific pharmacological profile. DISCUSSION Two distinct mammalian SphK isoforms have been identified, SphK1 and SphK2. These isoforms are encoded by different genes and exhibit distinct subcellular localizations, biochemical properties and functions. SphK1 and SphK2 inhibition can be useful in different pathological conditions. CONCLUSION SphK1 and SphK2 have many common features but different and even opposite biological functions. For this reason, several research groups are interested in understanding the therapeutic usefulness of a selective or non-selective inhibitor of SphKs. Moreover, a compensatory mechanism for the two isoforms has been demonstrated, thus leading to the development of dual inhibitors.
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Affiliation(s)
- Elisa Magli
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Angela Corvino
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Ferdinando Fiorino
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Francesco Frecentese
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Elisa Perissutti
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Irene Saccone
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Vincenzo Santagada
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Giuseppe Caliendo
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Beatrice Severino
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Naples, Italy
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Adams DR, Tawati S, Berretta G, Rivas PL, Baiget J, Jiang Z, Alsfouk A, Mackay SP, Pyne NJ, Pyne S. Topographical Mapping of Isoform-Selectivity Determinants for J-Channel-Binding Inhibitors of Sphingosine Kinases 1 and 2. J Med Chem 2019; 62:3658-3676. [DOI: 10.1021/acs.jmedchem.9b00162] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- David R. Adams
- School of Engineering & Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K
| | - Salha Tawati
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, U.K
| | - Giacomo Berretta
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, U.K
| | - Paula Lopez Rivas
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, U.K
| | - Jessica Baiget
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, U.K
| | - Zhong Jiang
- School of Engineering & Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K
| | - Aisha Alsfouk
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, U.K
| | - Simon P. Mackay
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, U.K
| | - Nigel J. Pyne
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, U.K
| | - Susan Pyne
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, U.K
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6
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Takahashi D, Sakane F. Expression and purification of human diacylglycerol kinase α from baculovirus-infected insect cells for structural studies. PeerJ 2018; 6:e5449. [PMID: 30128205 PMCID: PMC6089211 DOI: 10.7717/peerj.5449] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/26/2018] [Indexed: 02/02/2023] Open
Abstract
Diacylglycerol kinases (DGKs) are lipid kinases that modulate the levels of lipid second messengers, diacylglycerol and phosphatidic acid. Recently, increasing attention has been paid to its α isozyme (DGKα) as a potential target for cancer immunotherapy. DGKα consists of the N-terminal regulatory domains including EF-hand motifs and C1 domains, and the C-terminal catalytic domain (DGKα-CD). To date, however, no structures of mammalian DGKs including their CDs have yet been reported, impeding our understanding on the catalytic mechanism of DGKs and the rational structure-based drug design. Here we attempted to produce DGKα-CD or a full-length DGKα using bacterial and baculovirus-insect cell expression system for structural studies. While several DGKα-CD constructs produced using both bacterial and insect cells formed insoluble or soluble aggregates, the full-length DGKα expressed in insect cells remained soluble and was purified to near homogeneity as a monomer with yields (1.3 mg/mL per one L cell culture) feasible for protein crystallization. Following enzymatic characterization showed that the purified DGKα is in fully functional state. We further demonstrated that the purified enzyme could be concentrated without any significant aggregation, and characterized its secondary structure by circular dichroism. Taken together, these results suggest that the presence of N-terminal regulatory domains suppress protein aggregation likely via their intramolecular interactions with DGKα-CD, and demonstrate that the baculovirus-insect cell expression of the full-length form of DGKα, not DGKα-CD alone, represents a promising approach to produce protein sample for structural studies of DGKα. Thus, our study will encourage future efforts to determine the crystal structure of DGK, which has not been determined since it was first identified in 1959.
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Affiliation(s)
- Daisuke Takahashi
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
| | - Fumio Sakane
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
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7
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Franks CE, Campbell ST, Purow BW, Harris TE, Hsu KL. The Ligand Binding Landscape of Diacylglycerol Kinases. Cell Chem Biol 2017; 24:870-880.e5. [PMID: 28712745 DOI: 10.1016/j.chembiol.2017.06.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/15/2017] [Accepted: 06/16/2017] [Indexed: 11/17/2022]
Abstract
Diacylglycerol kinases (DGKs) are integral components of signal transduction cascades that regulate cell biology through ATP-dependent phosphorylation of the lipid messenger diacylglycerol. Methods for direct evaluation of DGK activity in native biological systems are lacking and needed to study isoform-specific functions of these multidomain lipid kinases. Here, we utilize ATP acyl phosphate activity-based probes and quantitative mass spectrometry to define, for the first time, ATP and small-molecule binding motifs of representative members from all five DGK subtypes. We use chemical proteomics to discover an unusual binding mode for the DGKα inhibitor, ritanserin, including interactions at the atypical C1 domain distinct from the ATP binding region. Unexpectedly, deconstruction of ritanserin yielded a fragment compound that blocks DGKα activity through a conserved binding mode and enhanced selectivity against the kinome. Collectively, our studies illustrate the power of chemical proteomics to profile protein-small molecule interactions of lipid kinases for fragment-based lead discovery.
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Affiliation(s)
- Caroline E Franks
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Sean T Campbell
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Benjamin W Purow
- Department of Neurology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Thurl E Harris
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
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8
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Tu-Sekine B, Goldschmidt HL, Raben DM. DGK-θ: Structure, Enzymology, and Physiological Roles. Front Cell Dev Biol 2016; 4:101. [PMID: 27683659 PMCID: PMC5021689 DOI: 10.3389/fcell.2016.00101] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/29/2016] [Indexed: 12/13/2022] Open
Abstract
Diacylglycerol kinases (DGKs) are a family of enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol (DAG) to phosphatidic acid (PtdOH). The recognition of the importance of these enzymes has been increasing ever since it was determined that they played a role in the phosphatidylinositol (PtdIns) cycle and a number of excellent reviews have already been written [(see van Blitterswijk and Houssa, 2000; Kanoh et al., 2002; Mérida et al., 2008; Tu-Sekine and Raben, 2009, 2011; Shulga et al., 2011; Tu-Sekine et al., 2013) among others]. We now know there are ten mammalian DGKs that are organized into five classes. DGK-θ is the lone member of the Type V class of DGKs and remains as one of the least studied. This review focuses on our current understanding of the structure, enzymology, regulation, and physiological roles of this DGK and suggests some future areas of research to understand this DGK isoform.
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Affiliation(s)
- Becky Tu-Sekine
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - Hana L Goldschmidt
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - Daniel M Raben
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine Baltimore, MD, USA
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9
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Sphingosine Kinases: Emerging Structure-Function Insights. Trends Biochem Sci 2016; 41:395-409. [PMID: 27021309 DOI: 10.1016/j.tibs.2016.02.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/08/2016] [Accepted: 02/17/2016] [Indexed: 12/15/2022]
Abstract
Sphingosine kinases (SK1 and SK2) catalyse the conversion of sphingosine into sphingosine 1-phosphate and control fundamental cellular processes, including cell survival, proliferation, differentiation, migration, and immune function. In this review, we highlight recent breakthroughs in the structural and functional characterisation of SK1 and these are contextualised by analysis of crystal structures for closely related prokaryotic lipid kinases. We identify a putative dimerisation interface and propose novel regulatory mechanisms governing structural plasticity induced by phosphorylation and interaction with phospholipids and proteins. Our analysis suggests that the catalytic function and regulation of the enzymes might be dependent on conformational mobility and it provides a roadmap for future interrogation of SK1 function and its role in physiology and disease.
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10
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Pyne S, Adams DR, Pyne NJ. Sphingosine 1-phosphate and sphingosine kinases in health and disease: Recent advances. Prog Lipid Res 2016; 62:93-106. [PMID: 26970273 DOI: 10.1016/j.plipres.2016.03.001] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/07/2016] [Accepted: 03/08/2016] [Indexed: 12/24/2022]
Abstract
Sphingosine kinases (isoforms SK1 and SK2) catalyse the formation of a bioactive lipid, sphingosine 1-phosphate (S1P). S1P is a well-established ligand of a family of five S1P-specific G protein coupled receptors but also has intracellular signalling roles. There is substantial evidence to support a role for sphingosine kinases and S1P in health and disease. This review summarises recent advances in the area in relation to receptor-mediated signalling by S1P and novel intracellular targets of this lipid. New evidence for a role of each sphingosine kinase isoform in cancer, the cardiovascular system, central nervous system, inflammation and diabetes is discussed. There is continued research to develop isoform selective SK inhibitors, summarised here. Analysis of the crystal structure of SK1 with the SK1-selective inhibitor, PF-543, is used to identify residues that could be exploited to improve selectivity in SK inhibitor development for future therapeutic application.
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Affiliation(s)
- Susan Pyne
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral St, Glasgow, G4 0RE, Scotland, UK.
| | - David R Adams
- School of Engineering & Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, Scotland, UK.
| | - Nigel J Pyne
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral St, Glasgow, G4 0RE, Scotland, UK.
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11
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A selective ATP-competitive sphingosine kinase inhibitor demonstrates anti-cancer properties. Oncotarget 2016; 6:7065-83. [PMID: 25788259 PMCID: PMC4466670 DOI: 10.18632/oncotarget.3178] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 01/25/2015] [Indexed: 12/20/2022] Open
Abstract
The dynamic balance of cellular sphingolipids, the sphingolipid rheostat, is an important determinant of cell fate, and is commonly deregulated in cancer. Sphingosine 1-phosphate is a signaling molecule with anti-apoptotic, pro-proliferative and pro-angiogenic effects, while conversely, ceramide and sphingosine are pro-apoptotic. The sphingosine kinases (SKs) are key regulators of this sphingolipid rheostat, and are attractive targets for anti-cancer therapy. Here we report a first-in-class ATP-binding site-directed small molecule SK inhibitor, MP-A08, discovered using an approach of structural homology modelling of the ATP-binding site of SK1 and in silico docking with small molecule libraries. MP-A08 is a highly selective ATP competitive SK inhibitor that targets both SK1 and SK2. MP-A08 blocks pro-proliferative signalling pathways, induces mitochondrial-associated apoptosis in a SK-dependent manner, and reduces the growth of human lung adenocarcinoma tumours in a mouse xenograft model by both inducing tumour cell apoptosis and inhibiting tumour angiogenesis. Thus, this selective ATP competitive SK inhibitor provides a promising candidate for potential development as an anti-cancer therapy, and also, due to its different mode of inhibition to other known SK inhibitors, both validates the SKs as targets for anti-cancer therapy, and represents an important experimental tool to study these enzymes.
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12
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Functional annotation of putative hypothetical proteins from Candida dubliniensis. Gene 2014; 543:93-100. [DOI: 10.1016/j.gene.2014.03.060] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Revised: 03/27/2014] [Accepted: 03/28/2014] [Indexed: 01/12/2023]
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13
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Maharjan RP, Gaffé J, Plucain J, Schliep M, Wang L, Feng L, Tenaillon O, Ferenci T, Schneider D. A case of adaptation through a mutation in a tandem duplication during experimental evolution in Escherichia coli. BMC Genomics 2013; 14:441. [PMID: 23822838 PMCID: PMC3708739 DOI: 10.1186/1471-2164-14-441] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 03/08/2013] [Indexed: 11/21/2022] Open
Abstract
Background DNA duplications constitute important precursors for genome variation. Here we analyzed an unequal duplication harboring a beneficial mutation that may provide alternative evolutionary outcomes. Results We characterized this evolutionary event during experimental evolution for only 100 generations of an Escherichia coli strain under glucose limitation within chemostats. By combining Insertion Sequence based Restriction Length Polymorphism experiments, pulsed field gel electrophoresis and two independent genome re-sequencing experiments, we identified an evolved lineage carrying a 180 kb duplication of the 46’ region of the E. coli chromosome. This evolved duplication revealed a heterozygous state, with one copy harboring a 2668 bp deletion that included part of the ogrK gene and both the yegR and yegS genes. By genetically manipulating ancestral and evolved strains, we showed that the single yegS inactivation was sufficient to confer a frequency dependent fitness increase under the chemostat selective conditions in both the ancestor and evolved genetic contexts, implying that the duplication itself was not a direct fitness contributor. Nonetheless, the heterozygous duplicated state was relatively stable in the conditions prevailing during evolution in chemostats, in striking contrast to non selective conditions in which the duplication resolved at high frequency into either its ancestral or deleted copy. Conclusions Our results suggest that the duplication state may constitute a second order selection process providing higher evolutionary potential. Moreover, its heterozygous nature may provide differential evolutionary opportunities in alternating environments. Our results also highlighted how careful analyses of whole genome data are needed to identify such complex rearrangements.
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Affiliation(s)
- Ram P Maharjan
- School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia
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14
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Wang Z, Min X, Xiao SH, Johnstone S, Romanow W, Meininger D, Xu H, Liu J, Dai J, An S, Thibault S, Walker N. Molecular basis of sphingosine kinase 1 substrate recognition and catalysis. Structure 2013; 21:798-809. [PMID: 23602659 DOI: 10.1016/j.str.2013.02.025] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 02/05/2013] [Accepted: 02/28/2013] [Indexed: 11/24/2022]
Abstract
Sphingosine kinase 1 (SphK1) is a lipid kinase that catalyzes the conversion of sphingosine to sphingosine-1-phosphate (S1P), which has been shown to play a role in lymphocyte trafficking, angiogenesis, and response to apoptotic stimuli. As a central enzyme in modulating the S1P levels in cells, SphK1 emerges as an important regulator for diverse cellular functions and a potential target for drug discovery. Here, we present the crystal structures of human SphK1 in the apo form and in complexes with a substrate sphingosine-like lipid, ADP, and an inhibitor at 2.0-2.3 Å resolution. The SphK1 structures reveal a two-domain architecture in which its catalytic site is located in the cleft between the two domains and a hydrophobic lipid-binding pocket is buried in the C-terminal domain. Comparative analysis of these structures with mutagenesis and kinetic studies provides insight into how SphK1 recognizes the lipid substrate and catalyzes ATP-dependent phosphorylation.
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Affiliation(s)
- Zhulun Wang
- Department of Molecular Structure and Characterization, Amgen, Inc., 1120 Veterans Boulevard, South San Francisco, CA 94080, USA.
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15
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Yan X, Shen Y. Preliminary crystallographic analysis of the kinase domain of SAD-1, a protein essential for presynaptic differentiation in Caenorhabditis elegans. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:449-52. [PMID: 23545657 PMCID: PMC3614176 DOI: 10.1107/s1744309113006088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 03/04/2013] [Indexed: 11/11/2022]
Abstract
SAD-1 is a serine/threonine kinase which plays an important role in the regulation of both neuronal polarity and synapse formation in Caenorhabditis elegans. The kinase domain of SAD-1 from C. elegans was overexpressed in Escherichia coli BL21 (DE3) cells and purified to homogeneity using nickel-nitrilotriacetic acid metal-affinity, ion-exchange and gel-filtration chromatography. Diffraction-quality crystals were grown using the sitting-drop vapour-diffusion technique from a condition consisting of 1 M CAPSO pH 9.6, 10%(w/v) polyethylene glycol 3350. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 205.4, b = 57.1, c = 71.7 Å, β = 106.1°. X-ray diffraction data were recorded to 3.0 Å resolution from a single crystal using synchrotron radiation.
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Affiliation(s)
- Xiaojie Yan
- Department of BMB, Basic Medical College, Tianjin Medical University, Tianjin 300070, People's Republic of China.
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Baker DL, Pham TCT, Sparks MA. Structure and catalytic function of sphingosine kinases: analysis by site-directed mutagenesis and enzyme kinetics. Biochim Biophys Acta Mol Cell Biol Lipids 2012; 1831:139-46. [PMID: 23000541 DOI: 10.1016/j.bbalip.2012.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 09/12/2012] [Accepted: 09/13/2012] [Indexed: 12/17/2022]
Abstract
Sphingosine kinases 1 and 2 (SK1 and SK2) generate the bioactive lipid mediator sphingosine 1-phosphate and as such play a significant role in cell fate and in human health and disease. Despite significant interest in and examination of the role played by SK enzymes in disease, comparatively little is currently known about the three-dimensional structure and catalytic mechanisms of these enzymes. To date, limited numbers of studies have used site directed mutagenesis and activity determinations to examine the roles of individual SK residues in substrate, calmodulin, and membrane binding, as well as activation via phosphorylation. Assays are currently available that allow for both single and bisubstrate kinetic analysis of mutant proteins that show normal, lowered and enhanced activity as compared to wild type controls. Additional studies will be required to build on this foundation to completely understand SK mediated substrate binding and phosphoryl group transfer. A deeper understanding of the SK catalytic mechanism, as well as SK interactions with potential small molecule inhibitors will be invaluable to the future design and identification of SK activity modulators as research tools and potential therapeutics. This article is part of a Special Issue entitled Advances in Lysophospholipid Research.
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Affiliation(s)
- Daniel L Baker
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA.
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Characterization of isoenzyme-selective inhibitors of human sphingosine kinases. PLoS One 2012; 7:e44543. [PMID: 22970244 PMCID: PMC3438171 DOI: 10.1371/journal.pone.0044543] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 08/07/2012] [Indexed: 12/22/2022] Open
Abstract
Sphingosine kinases (SKs) are promising new therapeutic targets for cancer because they regulate the balance between pro-apoptotic ceramides and mitogenic sphingosine-1-phosphate. The functions of the two SK isoenzymes, SK1 and SK2, are not redundant, with genetic ablation of SK2 having more pronounced anticancer effects than removal of SK1. Although several small molecule inhibitors of SKs have been described in the literature, detailed characterization of their molecular and cellular pharmacology, particularly their activities against human SK1 and SK2, have not been completed. Computational modeling of the putative active sites of SK1 and SK2 suggests structural differences that might allow isozyme-selective inhibitors. Therefore, we characterized several SK-inhibitory compounds which revealed differential inhibitory effects on SK1 and SK2 as follows: SKI-II and ABC294735 are SK1/2-dual inhibitors; CB5468139 is a SK1-selective inhibitor; and ABC294640 is a SK2-selective inhibitor. We examined the effects of the SK inhibitors on several biochemical and phenotypic processes in A498 kidney adenocarcinoma cells. The SK2-selective inhibitor ABC294640 demonstrated the most pronounced effects on SK1 and SK2 mRNA expression, decrease of S1P levels, elevation of ceramide levels, cell cycle arrest, and inhibition of proliferation, migration and invasion. ABC294640 also down-regulated the expression or activation of several signaling proteins, including STAT3, AKT, ERK, p21, p53 and FAK. These effects were equivalent or superior to responses to the SK1/2-dual inhibitors. Overall, these results suggest that inhibition of SK2 results in stronger anticancer effects than does inhibition of SK1 or both SK1 and SK2.
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Crystal structure of LpxK, the 4'-kinase of lipid A biosynthesis and atypical P-loop kinase functioning at the membrane interface. Proc Natl Acad Sci U S A 2012; 109:12956-61. [PMID: 22826246 DOI: 10.1073/pnas.1206072109] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
In Gram-negative bacteria, the hydrophobic anchor of the outer membrane lipopolysaccharide is lipid A, a saccharolipid that plays key roles in both viability and pathogenicity of these organisms. The tetraacyldisaccharide 4'-kinase (LpxK) of the diverse P-loop-containing nucleoside triphosphate hydrolase superfamily catalyzes the sixth step in the biosynthetic pathway of lipid A, and is the only known P-loop kinase to act upon a lipid substrate at the membrane. Here, we report the crystal structures of apo- and ADP/Mg(2+)-bound forms of Aquifex aeolicus LpxK to a resolution of 1.9 Å and 2.2 Å, respectively. LpxK consists of two α/β/α sandwich domains connected by a two-stranded β-sheet linker. The N-terminal domain, which has most structural homology to other family members, is responsible for catalysis at the P-loop and positioning of the disaccharide-1-phosphate substrate for phosphoryl transfer on the inner membrane. The smaller C-terminal domain, a substructure unique to LpxK, helps bind the nucleotide substrate and Mg(2+) cation using a 25° hinge motion about its base. Activity was severely reduced in alanine point mutants of conserved residues D138 and D139, which are not directly involved in ADP or Mg(2+) binding in our structures, indicating possible roles in phosphoryl acceptor positioning or catalysis. Combined structural and kinetic studies have led to an increased understanding of the enzymatic mechanism of LpxK and provided the framework for structure-based antimicrobial design.
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Orr Gandy KA, Obeid LM. Targeting the sphingosine kinase/sphingosine 1-phosphate pathway in disease: review of sphingosine kinase inhibitors. Biochim Biophys Acta Mol Cell Biol Lipids 2012; 1831:157-66. [PMID: 22801037 DOI: 10.1016/j.bbalip.2012.07.002] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/05/2012] [Accepted: 07/06/2012] [Indexed: 12/01/2022]
Abstract
Sphingosine 1-phosphate (S1P) is an important bioactive sphingolipid metabolite that has been implicated in numerous physiological and cellular processes. Not only does S1P play a structural role in cells by defining the components of the plasma membrane, but in the last 20 years it has been implicated in various significant cell signaling pathways and physiological processes: for example, cell migration, survival and proliferation, cellular architecture, cell-cell contacts and adhesions, vascular development, atherosclerosis, acute pulmonary injury and respiratory distress, inflammation and immunity, and tumorogenesis and metastasis [1,2]. Given the wide variety of cellular and physiological processes in which S1P is involved, it is immediately obvious why the mechanisms governing S1P synthesis and degradation, and the manner in which these processes are regulated, are necessary to understand. In gaining more knowledge about regulation of the sphingosine kinase (SK)/S1P pathway, many potential therapeutic targets may be revealed. This review explores the roles of the SK/S1P pathway in disease, summarizes available SK enzyme inhibitors and examines their potential as therapeutic agents. This article is part of a Special Issue entitled Advances in Lysophospholipid Research.
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Affiliation(s)
- K Alexa Orr Gandy
- The Department of Molecular and Cellular Biology, The Medical University of South Carolina, Charleston, SC 29425, USA
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Lim KG, Tonelli F, Berdyshev E, Gorshkova I, Leclercq T, Pitson SM, Bittman R, Pyne S, Pyne NJ. Inhibition kinetics and regulation of sphingosine kinase 1 expression in prostate cancer cells: functional differences between sphingosine kinase 1a and 1b. Int J Biochem Cell Biol 2012; 44:1457-64. [PMID: 22634604 DOI: 10.1016/j.biocel.2012.05.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Revised: 05/02/2012] [Accepted: 05/15/2012] [Indexed: 11/24/2022]
Abstract
Sphingosine kinase 1 catalyses the formation of the bioactive lipid, sphingosine 1-phosphate and is a target for anti-cancer agents. We demonstrate here that 2-(p-hydroxyanilino)-4-(p-chlorophenyl)thiazole (SKi, also referred to as SKI-II), FTY720 (Fingolimod), and (S)-FTY720 vinylphosphonate inhibit sphingosine kinase 1 activity with distinct kinetics, indicating that these compounds exhibit different binding modalities with sphingosine kinase 1. Thus, SKi is a mixed inhibitor of sphingosine and ATP binding, whereas FTY720 is competitive with sphingosine and uncompetitive with ATP, and (S)-FTY720 vinylphosphonate is uncompetitive with sphingosine and is a mixed inhibitor with respect to ATP. A novel 'see-saw' model is proposed for the binding of inhibitor to catalytic and allosteric sites, the latter dependent on substrate binding, that provides an explanation for the different inhibitor kinetics. In addition, we demonstrate that the expression level and properties unique to an N-terminal 86 amino-acid isoform variant of sphingosine kinase 1 (SK1b) in prostate cancer cells reduce its sensitivity to SKi-induced proteasomal degradation in comparison to SK1a, i.e. these two N-terminal variants of sphingosine kinase 1 (SK1a and SK1b) have different properties. The reduced sensitivity of SK1b to proteasomal degradation in response to SKi is translated into specific changes in ceramide and S1P levels that leads to apoptosis of androgen-sensitive but not androgen-independent LNCaP prostate cancer cells. Therefore, our proposed 'see-saw' model might be usefully employed in the design of sphingosine kinase inhibitors to promote apoptosis of chemotherapeutic resistant cancer cells.
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Affiliation(s)
- Keng Gat Lim
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, Glasgow, UK
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21
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Shaping up the membrane: diacylglycerol coordinates spatial orientation of signaling. Trends Biochem Sci 2011; 36:593-603. [PMID: 21798744 DOI: 10.1016/j.tibs.2011.06.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2011] [Revised: 06/21/2011] [Accepted: 06/23/2011] [Indexed: 11/23/2022]
Abstract
Diacylglycerol signals by binding and activating C1 domain-containing proteins expressed principally in neuronal and immune tissues. This restricted expression profile suggests that diacylglycerol-regulated signals are particularly relevant in cell-cell communication processes in which active endocytosis and exocytosis take place. Not surprisingly, various experimental approaches have demonstrated a crucial role for diacylglycerol effectors and metabolizing enzymes in the control of immune responses, neuron communication and phagocytosis. Current research delineates a scenario in which coordinated decoding of diacylglycerol signals is translated into complex biological responses such as neuronal plasticity, T cell development or cytolytic killing. Diacylglycerol functions reach maximal diversity in these highly specialized systems in which signal intensity directly regulates distinct biological outcomes. This review brings together the most recent studies, emphasizing the contribution of compartmentalized DAG metabolism to orientated signaling events.
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Kennedy AJ, Mathews TP, Kharel Y, Field SD, Moyer ML, East JE, Houck JD, Lynch KR, Macdonald TL. Development of amidine-based sphingosine kinase 1 nanomolar inhibitors and reduction of sphingosine 1-phosphate in human leukemia cells. J Med Chem 2011; 54:3524-48. [PMID: 21495716 DOI: 10.1021/jm2001053] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sphingosine 1-phosphate (S1P) is a bioactive lipid that has been identified as an accelerant of cancer progression. The sphingosine kinases (SphKs) are the sole producers of S1P, and thus, SphK inhibitors may prove effective in cancer mitigation and chemosensitization. Of the two SphKs, SphK1 overexpression has been observed in a myriad of cancer cell lines and tissues and has been recognized as the presumptive target over that of the poorly characterized SphK2. Herein, we present the design and synthesis of amidine-based nanomolar SphK1 subtype-selective inhibitors. A homology model of SphK1, trained with this library of amidine inhibitors, was then used to predict the activity of additional, more potent, inhibitors. Lastly, select amidine inhibitors were validated in human leukemia U937 cells, where they significantly reduced endogenous S1P levels at nanomolar concentrations.
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Affiliation(s)
- Andrew J Kennedy
- Department of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904, United States.
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23
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Pitson SM. Regulation of sphingosine kinase and sphingolipid signaling. Trends Biochem Sci 2011; 36:97-107. [DOI: 10.1016/j.tibs.2010.08.001] [Citation(s) in RCA: 217] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2010] [Revised: 08/16/2010] [Accepted: 08/16/2010] [Indexed: 01/09/2023]
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Lindner SN, Niederholtmeyer H, Schmitz K, Schoberth SM, Wendisch VF. Polyphosphate/ATP-dependent NAD kinase of Corynebacterium glutamicum: biochemical properties and impact of ppnK overexpression on lysine production. Appl Microbiol Biotechnol 2010; 87:583-93. [PMID: 20180116 DOI: 10.1007/s00253-010-2481-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 01/28/2010] [Accepted: 01/28/2010] [Indexed: 11/24/2022]
Abstract
Nicotinamide adenine dinucleotide phosphate (NADP) is synthesized by phosphorylation of either oxidized or reduced nicotinamide adenine dinucleotide (NAD/NADH). Here, the cg1601/ppnK gene product from Corynebacterium glutamicum genome was purified from recombinant Escherichia coli and enzymatic characterization revealed its activity as a polyphosphate (PolyP)/ATP-dependent NAD kinase (PPNK). PPNK from C. glutamicum was shown to be active as homotetramer accepting PolyP, ATP, and even ADP for phosphorylation of NAD. The catalytic efficiency with ATP as phosphate donor for phosphorylation of NAD was higher than with PolyP. With respect to the chain length of PolyP, PPNK was active with short-chain PolyPs. PPNK activity was independent of bivalent cations when using ATP, but was enhanced by manganese and in particular by magnesium ions. When using PolyP, PPNK required bivalent cations, preferably manganese ions, for activity. PPNK was inhibited by NADP and NADH at concentrations below millimolar. Overexpression of ppnK in C. glutamicum wild type slightly reduced growth and ppnK overexpression in the lysine producing strain DM1729 resulted in a lysine product yield on glucose of 0.136 +/- 0.006 mol lysine (mol glucose)(-1), which was 12% higher than that of the empty vector control strain.
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Affiliation(s)
- Steffen N Lindner
- Institute of Molecular Microbiology and Biotechnology, Westfalian Wilhelms University Muenster, 48149, Muenster, Germany
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25
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Chen WQ, Graf C, Zimmel D, Rovina P, Krapfenbauer K, Jaritz M, Parker PJ, Lubec G, Bornancin F. Ceramide Kinase Profiling by Mass Spectrometry Reveals a Conserved Phosphorylation Pattern Downstream of the Catalytic Site. J Proteome Res 2009; 9:420-9. [DOI: 10.1021/pr900763z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wei-Qiang Chen
- Department of Pediatrics, Medical University of Vienna, Waehringer Guertel 18, A-1090, Vienna, Austria, Novartis Institutes for BioMedical Research (NIBR), Vienna, Brunnerstrasse 59, A-1235 Vienna, Austria, Protein Phosphorylation Laboratory, London Research Institute, Cancer Research U.K., London, WC2A 3PX, United Kingdom, and the Division of Cancer Studies King’s College London, New Hunt’s House, Guy’s Hospital, St Thomas Street, London SE1 1UL, United Kingdom
| | - Christine Graf
- Department of Pediatrics, Medical University of Vienna, Waehringer Guertel 18, A-1090, Vienna, Austria, Novartis Institutes for BioMedical Research (NIBR), Vienna, Brunnerstrasse 59, A-1235 Vienna, Austria, Protein Phosphorylation Laboratory, London Research Institute, Cancer Research U.K., London, WC2A 3PX, United Kingdom, and the Division of Cancer Studies King’s College London, New Hunt’s House, Guy’s Hospital, St Thomas Street, London SE1 1UL, United Kingdom
| | - David Zimmel
- Department of Pediatrics, Medical University of Vienna, Waehringer Guertel 18, A-1090, Vienna, Austria, Novartis Institutes for BioMedical Research (NIBR), Vienna, Brunnerstrasse 59, A-1235 Vienna, Austria, Protein Phosphorylation Laboratory, London Research Institute, Cancer Research U.K., London, WC2A 3PX, United Kingdom, and the Division of Cancer Studies King’s College London, New Hunt’s House, Guy’s Hospital, St Thomas Street, London SE1 1UL, United Kingdom
| | - Philipp Rovina
- Department of Pediatrics, Medical University of Vienna, Waehringer Guertel 18, A-1090, Vienna, Austria, Novartis Institutes for BioMedical Research (NIBR), Vienna, Brunnerstrasse 59, A-1235 Vienna, Austria, Protein Phosphorylation Laboratory, London Research Institute, Cancer Research U.K., London, WC2A 3PX, United Kingdom, and the Division of Cancer Studies King’s College London, New Hunt’s House, Guy’s Hospital, St Thomas Street, London SE1 1UL, United Kingdom
| | - Kurt Krapfenbauer
- Department of Pediatrics, Medical University of Vienna, Waehringer Guertel 18, A-1090, Vienna, Austria, Novartis Institutes for BioMedical Research (NIBR), Vienna, Brunnerstrasse 59, A-1235 Vienna, Austria, Protein Phosphorylation Laboratory, London Research Institute, Cancer Research U.K., London, WC2A 3PX, United Kingdom, and the Division of Cancer Studies King’s College London, New Hunt’s House, Guy’s Hospital, St Thomas Street, London SE1 1UL, United Kingdom
| | - Markus Jaritz
- Department of Pediatrics, Medical University of Vienna, Waehringer Guertel 18, A-1090, Vienna, Austria, Novartis Institutes for BioMedical Research (NIBR), Vienna, Brunnerstrasse 59, A-1235 Vienna, Austria, Protein Phosphorylation Laboratory, London Research Institute, Cancer Research U.K., London, WC2A 3PX, United Kingdom, and the Division of Cancer Studies King’s College London, New Hunt’s House, Guy’s Hospital, St Thomas Street, London SE1 1UL, United Kingdom
| | - Peter J. Parker
- Department of Pediatrics, Medical University of Vienna, Waehringer Guertel 18, A-1090, Vienna, Austria, Novartis Institutes for BioMedical Research (NIBR), Vienna, Brunnerstrasse 59, A-1235 Vienna, Austria, Protein Phosphorylation Laboratory, London Research Institute, Cancer Research U.K., London, WC2A 3PX, United Kingdom, and the Division of Cancer Studies King’s College London, New Hunt’s House, Guy’s Hospital, St Thomas Street, London SE1 1UL, United Kingdom
| | - Gert Lubec
- Department of Pediatrics, Medical University of Vienna, Waehringer Guertel 18, A-1090, Vienna, Austria, Novartis Institutes for BioMedical Research (NIBR), Vienna, Brunnerstrasse 59, A-1235 Vienna, Austria, Protein Phosphorylation Laboratory, London Research Institute, Cancer Research U.K., London, WC2A 3PX, United Kingdom, and the Division of Cancer Studies King’s College London, New Hunt’s House, Guy’s Hospital, St Thomas Street, London SE1 1UL, United Kingdom
| | - Frédéric Bornancin
- Department of Pediatrics, Medical University of Vienna, Waehringer Guertel 18, A-1090, Vienna, Austria, Novartis Institutes for BioMedical Research (NIBR), Vienna, Brunnerstrasse 59, A-1235 Vienna, Austria, Protein Phosphorylation Laboratory, London Research Institute, Cancer Research U.K., London, WC2A 3PX, United Kingdom, and the Division of Cancer Studies King’s College London, New Hunt’s House, Guy’s Hospital, St Thomas Street, London SE1 1UL, United Kingdom
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26
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Lidome E, Graf C, Jaritz M, Schanzer A, Rovina P, Nikolay R, Bornancin F. A conserved cysteine motif essential for ceramide kinase function. Biochimie 2008; 90:1560-5. [PMID: 18662741 DOI: 10.1016/j.biochi.2008.07.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Accepted: 07/03/2008] [Indexed: 11/18/2022]
Abstract
Ceramide kinase (CerK) is a sphingolipid metabolizing enzyme very sensitive to oxidation; however, the determinants are unknown. We show here that the thiol-modifying agent N-ethyl-maleimide abrogates CerK activity in vitro and in a cell based assay, implying that important cysteine residues are accessible in purified as well as endogenous CerK. We replaced every 22 residues in human CerK, by an alanine, and measured activity in the resulting mutant proteins. This led to identification of a cluster of cysteines, C(347)XXXC(351)XXC(354), essential for CerK function. These findings are discussed based on homology modeling of the catalytic domain of CerK.
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Affiliation(s)
- Emilie Lidome
- Novartis Institutes for BioMedical Research, Vienna, Vienna, Austria
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27
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Miller DJ, Jerga A, Rock CO, White SW. Analysis of the Staphylococcus aureus DgkB structure reveals a common catalytic mechanism for the soluble diacylglycerol kinases. Structure 2008; 16:1036-46. [PMID: 18611377 PMCID: PMC2847398 DOI: 10.1016/j.str.2008.03.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 03/26/2008] [Accepted: 03/28/2008] [Indexed: 10/21/2022]
Abstract
Soluble diacylglycerol (DAG) kinases function as regulators of diacylglycerol metabolism in cell signaling and intermediary metabolism. We report the structure of a DAG kinase, DgkB from Staphylococcus aureus, both as the free enzyme and in complex with ADP. The molecule is a tight homodimer, and each monomer comprises two domains with the catalytic center located within the interdomain cleft. Two distinctive features of DkgB are a structural Mg2+ site and an associated Asp*water*Mg2+ network that extends toward the active site locale. Site-directed mutagenesis revealed that these features play important roles in the catalytic mechanism. The key active site residues and the components of the Asp*water*Mg2+ network are conserved in the catalytic cores of the mammalian signaling DAG kinases, indicating that these enzymes use the same mechanism and have similar structures as DgkB.
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Affiliation(s)
- Darcie J. Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, 332 North Lauderdale St., Memphis, TN 38105-2794, U.S.A
| | - Agoston Jerga
- Department of Infectious Diseases, St. Jude Children's Research Hospital, 332 North Lauderdale St., Memphis, TN 38105-2794, U.S.A
| | - Charles O. Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, 332 North Lauderdale St., Memphis, TN 38105-2794, U.S.A
- Department of Molecular Sciences, University of Tennessee Health Science Center, Memphis, TN 38163. Correspondence should be addressed to S.W.W. () and C.O.R ()
| | - Stephen W. White
- Department of Structural Biology, St. Jude Children's Research Hospital, 332 North Lauderdale St., Memphis, TN 38105-2794, U.S.A
- Department of Molecular Sciences, University of Tennessee Health Science Center, Memphis, TN 38163. Correspondence should be addressed to S.W.W. () and C.O.R ()
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28
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Graf C, Niwa S, Müller M, Kinzel B, Bornancin F. Wild-type levels of ceramide and ceramide-1-phosphate in the retina of ceramide kinase-like-deficient mice. Biochem Biophys Res Commun 2008; 373:159-63. [PMID: 18555012 DOI: 10.1016/j.bbrc.2008.06.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Accepted: 06/04/2008] [Indexed: 11/18/2022]
Abstract
Ceramide kinase-like (CerkL) is the most recently identified member of the sphingolipid metabolizing enzyme family. This protein is believed to have ceramide kinase (CerK) activity; however, this has not been clarified yet. We generated CerkL-deficient (CerkL(-/-)) mice, measured ceramide (Cer) and ceramide-1-phosphate (C1P) levels in isolated retina, and compared them to levels measured in Cerk(-/-) and WT retinas. We also labeled CerkL(-/-), Cerk(-/-), and WT retinas with (33)P orthophosphate to measure and compare de novo phosphorylation of Cer. Whereas Cerk(-/-) retinas displayed decreased C1P and enhanced Cer, and lacked the capacity to phosphorylate Cer, CerkL(-/-) retinas were indistinguishable from WT retinas with regard to Cer and C1P levels, and in their ability to phosphorylate Cer. Altogether, our results do not support the hypothesis that CerkL is a second CerK enzyme impacting on Cer levels in the retina. CerkL, if active enzymatically, might use a novel, not yet described, lipid substrate.
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Affiliation(s)
- Christine Graf
- Novartis Institutes for BioMedical Research, Brunnerstrasse 59, A-1235 Vienna, Austria
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29
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Poncet-Montange G, Assairi L, Arold S, Pochet S, Labesse G. NAD kinases use substrate-assisted catalysis for specific recognition of NAD. J Biol Chem 2007; 282:33925-34. [PMID: 17686780 DOI: 10.1074/jbc.m701394200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Here we describe the crystal structures of the NAD kinase (LmNADK1) from Listeria monocytogenes in complex with its substrate NAD, its product NADP, or two synthesized NAD mimics. We identified one of the NAD mimics, di-adenosine diphosphate, as a new substrate for LmNADK1, whereas we showed that the closely related compound di-5'-thioadenosine is a novel non-natural inhibitor for this enzyme. These structures suggest a mechanism involving substrate-assisted catalysis. Indeed, sequence/structure comparison and directed mutagenesis have previously shown that NAD kinases (NADKs) and the distantly related 6-phosphofructokinases share the same catalytically important GGDGT motif. However, in this study we have shown that these enzymes use the central aspartate of this motif differently. Although this acidic residue chelates the catalytic Mg(2+) ion in 6-phosphofructokinases, it activates the phospho-acceptor (NAD) in NADKs. Sequence/structure comparisons suggest that the role of this aspartate would be conserved in NADKs and the related sphingosine and diacylglycerol kinases.
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Affiliation(s)
- Guillaume Poncet-Montange
- Atelier de Bio- et Chimie Informatique Structurale, Centre de Biochimie Structurale, UMR 5048/CNRS, Universités Montpellier 1 et 2, 29 rue de Navacelles, Montpellier, France
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30
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Jerga A, Lu YJ, Schujman GE, de Mendoza D, Rock CO. Identification of a soluble diacylglycerol kinase required for lipoteichoic acid production in Bacillus subtilis. J Biol Chem 2007; 282:21738-45. [PMID: 17535816 DOI: 10.1074/jbc.m703536200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Diacylglycerol kinases (DagKs) are key enzymes in lipid metabolism that function to reintroduce diacylglycerol formed from the hydrolysis of phospholipids into the biosynthetic pathway. Bacillus subtilis is a prototypical Gram-positive bacterium with a lipoteichoic acid structure containing repeating units of sn-glycerol-1-P groups derived from phosphatidylglycerol head groups. The B. subtilis homolog of the prokaryotic DagK gene family (dgkA; Pfam01219) was not a DagK but rather was an undecaprenol kinase. The three members of the soluble DagK protein family (Pfam00781) in B. subtilis were tested by complementation of an E. coli dgkA mutant, and only the essential yerQ gene possessed DagK activity. This gene was dubbed dgkB, and the soluble protein product was purified, and its DagK activity was verified in vitro. Conditional inactivation of dgkB led to the accumulation of diacylglycerol and the cessation of lipoteichoic acid formation in B. subtilis. This study identifies a soluble protein encoded by the dgkB (yerQ) gene as an essential kinase in the diacylglycerol cycle that drives lipoteichoic acid production.
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Affiliation(s)
- Agoston Jerga
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105-2794, USA
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